CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of PPfold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Multilign(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PPfold(20) & Multilign(seed) [.zip] - may take several seconds...

Overview

Metric	PPfold(20)		Multilign(seed)
MCC	0.703	>	0.678
Average MCC ± 95% Confidence Intervals	0.694 ± 0.079	<	0.711 ± 0.265
Sensitivity	0.543	=	0.543
Positive Predictive Value	0.915	>	0.852
Total TP	75	=	75
Total TN	11406	>	11400
Total FP	8	<	14
Total FP CONTRA	0	<	1
Total FP INCONS	7	<	12
Total FP COMP	1	=	1
Total FN	63	=	63
P-value	0.0

Performance plots

Performance of PPfold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PPfold(20)

Total Base Pair Counts
Total TP	75
Total TN	11406
Total FP	8
Total FP CONTRA	0
Total FP INCONS	7
Total FP COMP	1
Total FN	63

Total Scores
MCC	0.703
Average MCC ± 95% Confidence Intervals	0.694 ± 0.079
Sensitivity	0.543
Positive Predictive Value	0.915
Nr of predictions	4

2. Individual counts for PPfold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.63	0.45	0.90	9	980	1	0	1	0	11
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17

Performance of Multilign(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for Multilign(seed)

Total Base Pair Counts
Total TP	75
Total TN	11400
Total FP	14
Total FP CONTRA	1
Total FP INCONS	12
Total FP COMP	1
Total FN	63

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.711 ± 0.265
Sensitivity	0.543
Positive Predictive Value	0.852
Nr of predictions	4

2. Individual counts for Multilign(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.85	1.00	17	973	0	0	0	0	3
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.55	0.45	0.68	19	3888	9	1	8	0	23
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.